Background: The optical coherence tomography (OCT) is an imaging modality, based on infrared light backscattering properties of tissues. OCT studies documented the disappearance of crypts and the alteration in light backscattering as features of ulcerative colitis (UC) in human colon. This technique should be more and more able to identify tissue microstructures with a resolution that is nearly that of histology (“optical biopsy”). The aim of this study was to evaluate whether there are OCT patterns specific for IBD and to compare the overall technique performance to the histology. Patients and Methods: 35 patients (18M/17F; mean age 48,3 years) with IBD (31UC/4CD) underwent OCT imaging during a total colonoscopy. The OCT images were collected both from affected and normal sites in active IBD or disease in remission. Two macrobiopsies of the same sites were acquired. The OCT images were separately scored. Two pathologists blinded to the endoscopic and OCT patterns performed the histologic evaluation. Results: Three OCT patterns were identified: the Mucosal Backscattering Alteration (MBA), the Delimited Dark Areas (DDA) and the Layered Colonic Wall (LCW). Compared to the gold standard, the MBA has shown the most effective in recognizing pathological features both in affected and normal colon segments of IBD patients (p = 0.007; p = 0.000). Thus, the overall sensitivity, specificity, NPV and PPV of MBA have been 100%, 83%, 100% and 72% respectively. In active CD, OCT documented the complete disruption of layered wall, due to the deep inflammation. Conclusions: In comparison with the histology, the in vivo-OCT correctly detected pathological features in endoscopically affected colon segments, but even in apparently normal segments of IBD patients. This technique allowed to discriminate patterns for active UC and CD, thus representing a promising modality in the differential diagnosis of IBD.